GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08235 in Herbaspirillum seropedicae SmR1

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate HSERO_RS05960 HSERO_RS05960 ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05960 HSERO_RS05960 ABC
           transporter permease
          Length = 309

 Score =  258 bits (658), Expect = 2e-73
 Identities = 133/307 (43%), Positives = 207/307 (67%), Gaps = 18/307 (5%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVAL-----ITFL 55
           M+ F+QQ+INGL LG++Y LIA+GYTMVYG++ +INFAHG+I M+GA V L     +  +
Sbjct: 1   MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60

Query: 56  AIGSLGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQ 115
           A G  GI    + L++ +V ++    V    +ERIAYRPLR++PRLAPLI+AIG+SI LQ
Sbjct: 61  APGLPGI----VQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQ 116

Query: 116 NYVQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGR 175
               ++ G    P   ++P +   + GA+ +S  ++  + + +  M G   ++ +T +GR
Sbjct: 117 TLAMMIWGRSPLPFPQVMPSDPVHIAGAL-ISPTQIMLLALAVLAMVGLVLIVEKTKMGR 175

Query: 176 AQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKA 235
           A RA  ++ ++AGL+GV+ ++VI +TF +GA LAA+AG+M    Y    F +GF+ G+KA
Sbjct: 176 AMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKA 235

Query: 236 FTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGY--------MGSEWKDVATFTILVLVLIF 287
           F+AAVLGGIG++ GAMLGG+++GLIE+  +GY        +GS ++D+  F +L++VL  
Sbjct: 236 FSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTL 295

Query: 288 RPTGLLG 294
           RP+G++G
Sbjct: 296 RPSGIMG 302


Lambda     K      H
   0.329    0.144    0.425 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 396
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 301
Length of database: 309
Length adjustment: 27
Effective length of query: 274
Effective length of database: 282
Effective search space:    77268
Effective search space used:    77268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory